Guhan Venkataraman
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View article: Genetics of cardiometabolic disease progression
Genetics of cardiometabolic disease progression Open
Background Genome-wide association studies have been crucial in gaining insights into the genetics of cardiometabolic diseases. However, little is known about the genetics of cardiometabolic disease progression which may have both a differ…
View article: Nanoparticle enrichment mass-spectrometry proteomics identifies protein-altering variants for precise pQTL mapping
Nanoparticle enrichment mass-spectrometry proteomics identifies protein-altering variants for precise pQTL mapping Open
View article: Identification of Novel Biomarkers for Alzheimer’s Disease and Related Dementias Using Unbiased Plasma Proteomics
Identification of Novel Biomarkers for Alzheimer’s Disease and Related Dementias Using Unbiased Plasma Proteomics Open
Alzheimer’s disease (AD) and related dementias (ADRD) is a complex disease with multiple pathophysiological drivers that determine clinical symptomology and disease progression. These diseases develop insidiously over time, through many pa…
View article: Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping
Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping Open
Genome-wide association studies (GWAS) with proteomics generate hypotheses on protein function and offer genetic evidence for drug target prioritization. Although most protein quantitative loci (pQTLs) have so far been identified by high-t…
View article: Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility
Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility Open
View article: Significant sparse polygenic risk scores across 813 traits in UK Biobank
Significant sparse polygenic risk scores across 813 traits in UK Biobank Open
We present a systematic assessment of polygenic risk score (PRS) prediction across more than 1,500 traits using genetic and phenotype data in the UK Biobank. We report 813 sparse PRS models with significant (p < 2.5 x 10 −5 ) incremental p…
View article: Bayesian model comparison for rare-variant association studies
Bayesian model comparison for rare-variant association studies Open
View article: Author Correction: Genetics of 35 blood and urine biomarkers in the UK Biobank
Author Correction: Genetics of 35 blood and urine biomarkers in the UK Biobank Open
View article: Significant Sparse Polygenic Risk Scores across 813 traits in UK Biobank
Significant Sparse Polygenic Risk Scores across 813 traits in UK Biobank Open
We present a systematic assessment of polygenic risk score (PRS) prediction across more than 1,500 traits using genetic and phenotype data in the UK Biobank. We report 813 sparse PRS models with significant (p < 2.5 × 10 −5 ) incremental p…
View article: Bayesian mixture model for clustering rare-variant effects in human genetic studies
Bayesian mixture model for clustering rare-variant effects in human genetic studies Open
Rare-variant aggregate analysis from exome and whole genome sequencing data typically summarizes with a single statistic the signal for a gene or the unit that is being aggregated. However, when doing so, the effect profile within the unit…
View article: Sequencing of over 100,000 individuals identifies multiple genes and rare variants associated with Crohns disease susceptibility
Sequencing of over 100,000 individuals identifies multiple genes and rare variants associated with Crohns disease susceptibility Open
Genome-wide association studies (GWAS) have identified hundreds of loci associated with Crohns disease (CD), however, as with all complex diseases, deriving pathogenic mechanisms from these non-coding GWAS discoveries has been challenging.…
View article: Polygenic risk modeling with latent trait-related genetic components
Polygenic risk modeling with latent trait-related genetic components Open
View article: Genetics of 35 blood and urine biomarkers in the UK Biobank
Genetics of 35 blood and urine biomarkers in the UK Biobank Open
View article: all_beta_center_p1e-06_20200506_500PCs.npz
all_beta_center_p1e-06_20200506_500PCs.npz Open
Final model weights for matrix Decomposition of Genetic Associations (DeGAs) using summary statistics from genome-wide association studies in UK Biobank. See referenced paper and project GitHub for model description and example use cases.
View article: A deep learning classifier for local ancestry inference
A deep learning classifier for local ancestry inference Open
Local ancestry inference (LAI) identifies the ancestry of each segment of an individual's genome and is an important step in medical and population genetic studies of diverse cohorts. Several techniques have been used for LAI, including Hi…
View article: Cardiac Imaging of Aortic Valve Area From 34 287 UK Biobank Participants Reveals Novel Genetic Associations and Shared Genetic Comorbidity With Multiple Disease Phenotypes
Cardiac Imaging of Aortic Valve Area From 34 287 UK Biobank Participants Reveals Novel Genetic Associations and Shared Genetic Comorbidity With Multiple Disease Phenotypes Open
Background: The aortic valve is an important determinant of cardiovascular physiology and anatomic location of common human diseases. Methods: From a sample of 34 287 white British ancestry participants, we estimated functional aortic valv…
View article: FasTag: Automatic text classification of unstructured medical narratives
FasTag: Automatic text classification of unstructured medical narratives Open
Unstructured clinical narratives are continuously being recorded as part of delivery of care in electronic health records, and dedicated tagging staff spend considerable effort manually assigning clinical codes for billing purposes. Despit…
View article: Pervasive additive and non-additive effects within the HLA region contribute to disease risk in the UK Biobank
Pervasive additive and non-additive effects within the HLA region contribute to disease risk in the UK Biobank Open
The human leukocyte antigen (HLA) region is one of the most disease-associated regions of the human genome, yet even well-studied alleles in the HLA region have unknown impact on disease. Here, we study the effect of 156 HLA alleles on 677…
View article: Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma
Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma Open
Protein-altering variants that are protective against human disease provide in vivo validation of therapeutic targets. Here we use genotyping data from UK Biobank (n = 337,151 unrelated White British individuals) and FinnGen (n = 176,899) …
View article: Cardiac imaging of aortic valve area from 26,142 UK Biobank participants reveal novel genetic associations and shared genetic comorbidity with multiple disease phenotypes
Cardiac imaging of aortic valve area from 26,142 UK Biobank participants reveal novel genetic associations and shared genetic comorbidity with multiple disease phenotypes Open
The aortic valve is an important determinant of cardiovascular physiology and anatomic location of common human diseases. From a sample of 26,142 European-ancestry participants, we estimated functional aortic valve area by planimetry from …
View article: Automated Classification of Radiographic Knee Osteoarthritis Severity Using Deep Neural Networks
Automated Classification of Radiographic Knee Osteoarthritis Severity Using Deep Neural Networks Open
An end-to-end interpretable model that takes full radiographs as input and predicts KL scores with state-of-the-art accuracy, performs as well as musculoskeletal radiologists, and does not require manual image preprocessing was developed. …
View article: Conditional random fields improve local ancestry model predictions
Conditional random fields improve local ancestry model predictions Open
View article: Medical relevance of common protein-altering variants in GPCR genes across 337,205 individuals in the UK Biobank
Medical relevance of common protein-altering variants in GPCR genes across 337,205 individuals in the UK Biobank Open
G protein-coupled receptors (GPCRs) drive an array of critical physiological functions and are an important class of drug targets, though a map of which GPCR genetic variants are associated with phenotypic variation is lacking. We performe…
View article: Polygenic risk modeling with latent trait-related genetic components
Polygenic risk modeling with latent trait-related genetic components Open
Polygenic risk models have led to significant advances in understanding complex diseases and their clinical presentation. While models like polygenic risk scores (PRS) can effectively predict outcomes, they do not generally account for dis…
View article: Rare and common variant discovery in complex disease: the IBD case study
Rare and common variant discovery in complex disease: the IBD case study Open
Complex diseases such as inflammatory bowel disease (IBD), which consists of ulcerative colitis and Crohn’s disease, are a significant medical burden—70 000 new cases of IBD are diagnosed in the United States annually. In this review, we e…
View article: Genetics of 38 blood and urine biomarkers in the UK Biobank
Genetics of 38 blood and urine biomarkers in the UK Biobank Open
Clinical laboratory tests are a critical component of the continuum of care and provide a means for rapid diagnosis and monitoring of chronic disease. In this study, we systematically evaluated the genetic basis of 38 blood and urine labor…
View article: Deep Learning Facilitates Rapid Cohort Identification Using Human and Veterinary Clinical Narratives
Deep Learning Facilitates Rapid Cohort Identification Using Human and Veterinary Clinical Narratives Open
View article: <i>DE NOVO</i> MUTATIONS IN AUTISM IMPLICATE THE SYNAPTIC ELIMINATION NETWORK
<i>DE NOVO</i> MUTATIONS IN AUTISM IMPLICATE THE SYNAPTIC ELIMINATION NETWORK Open
Autism has been shown to have a major genetic risk component; the architecture of documented autism in families has been over and again shown to be passed down for generations. While inherited risk plays an important role in the autistic n…